Sequence editor that can delete columns?

Jeremy Packer jclp100 at mole.bio.cam.ac.uk
Thu Feb 27 04:21:53 EST 1997


>ac562 at freenet.carleton.ca (Robert J. Forster) wrote:
>>I have quite a few alignments of 16S rRNA sequences from which I would
>>like to delete a highly variable region before analysis.  I have used
>>ClustalX and Seqpup on a mac to produce the alignments. When I select a
>>block of sequences in seqpup and then hit the Edit clear or cut
>>functions nothing happens.  I can delete the region one sequence at a
>>time, but with hundreds of sequences I am searching for an easier way.
>>I have put GDE on an HP-UX machine and DCSE on Linux, but both of these
>>installations are not exactly stable, and the documentation for these
>>programs does not indicate whether the proposed task would be very easy.
>>If anyone knows of a program that could help me out I would appreciate
>>some pointers.
>>
I use Microsoft Word now (thanks to a response in this Newsgroup to the same Qu several months ago). Reformat the alignment into a proportional font (courier, 9pt). Highlight columns by moving the cursor to one corner of the block and then clicking the opposite corner while holding down the alt and shift keys, or else by moving the mouse while holding the above keys and the button down. The highlighted block can then be cut (and pasted) as usual.






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